基于转录组数据挖掘牦牛皱胃发育代谢的关键候选基因  

Mining Key Candidate Genes of Development and Metabolism in Yak Abomasum Based on Transcriptome Data

作　　者：刘益丽[1] 唐娇 闵奇 杨露 王泽宁 胡莲 赵迪 江明锋[1] LIU Yili;TANG Jiao;MIN Qi;YANG Lu;WANG Zening;HU Lian;ZHAO Di;JIANG Mingfeng(College of Animal&Veterinary Sciences,Southwest Minzu University,Chengdu 610041,China;Institute of Qinghai-Tibetan Plateau,Southwest Minzu University,Chengdu 610041,China)

机构地区：[1]西南民族大学畜牧兽医学院,成都610041 [2]西南民族大学青藏高原研究院,成都610041

出　　处：《畜牧兽医学报》2024年第1期153-168,共16页ACTA VETERINARIA ET ZOOTECHNICA SINICA

基　　金：四川省自然科学基金项目(2022NSFSC1665);西南民族大学科研启动金资助项目(RQD2022048);四川省区域创新合作项目(2023YFQ0076);四川省重点研发项目(2021YFYZ0001,2021YFN0001)。

摘　　要：旨在比较不同年龄段牦牛皱胃指数测定、转录组表达谱的变化,挖掘影响牦牛皱胃发育代谢的信号通路和关键基因,为进一步探讨牦牛皱胃发育机制提供理论基础。本研究对1日龄、20日龄、60日龄、15月龄与3岁的牦牛皱胃组织进行转录组测序,对转录组数据进行质控、比对、差异表达基因筛选,并对差异表达基因进行GO功能注释和KEGG富集分析。为进一步验证测序数据的可靠性,随机选取5个差异表达基因进行qRT-PCR验证。结果显示,在发育过程中,瘤胃重的增长最快,其次是瓣胃、网胃和皱胃。转录组结果显示,以1日龄组为对照,在20日龄、60日龄、15月龄和3岁组中分别鉴定到1310、1715、1931和2199个差异表达基因,4个组共有基因565个;以前一个时间点为对照,20日龄、60日龄、15月龄和3岁组分别鉴定到1310、861、569和597个差异表达基因,4个对比组共有基因9个。GO功能注释发现,以1日龄组为对照,20日龄、60日龄、15月龄和3岁组分别富集到1191、2578、1117和2835条显著条目,不同年龄组的前10条显著性GO条目中有共有的,也有各年龄阶段特有的条目。KEGG富集分析结果显示,20日龄、60日龄、15月龄和3岁4个年龄段的前30条显著通路中特有信号通路分别为4、1、3和4条,包括ECM受体相互作用、细胞色素P450对外源性物质的代谢和药物代谢-细胞色素P450等与皱胃发育相关的通路。qRT-PCR结果与测序结果基本一致,表明测序结果可靠。通过对牦牛不同发育阶段皱胃组织的转录组测序及生物信息学分析,筛选到与皱胃发育相关的差异表达候选基因,这些基因主要参与胃粘膜上皮细胞增殖分化、细胞分化和免疫调控等过程,其中GKN1、CXCL17、SCNN 1B、SCNN 1G、CCL 5和IGF 2BP3等基因可能在牦牛皱胃发育过程中起着重要作用;进一步筛选到参与皱胃葡萄糖代谢、葡萄糖转运、脂肪酸转运、肽转运等过程相�This study aimed to compare the changes in abomasum index and transcriptome expression profile of yaks at different ages,and to explore the signaling pathways and key genes that affect the development and metabolism of abomasum,so as to provide theoretical basis for further study of development mechanism of abomasum in yaks.Abomasum tissues of yaks at 1 day,20 days,60 days,15 months and 3 years old were selected for transcriptome sequencing.The RNA-Seq data were performed quality-controlled,alignment,differential genes screening;GO and KEGG analysis were conducted for differentially expressed genes(DEGs).To further verify the reliability of sequencing data,5 DEGs were randomly selected for qRT-PCR verification.The results showed that rumen weight increased the fastest,followed by omasum,reticulum and abomasum during development.Compared with 1 day,1310,1715,1931 and 2199 DEGs were identified at 20 days,60 days,15 months and 3 years old,respectively.A total of 565 DEGs were defined as common DEGs among 4 closed groups.Compared with the previous time point,1310,861,569 and 597 DEGs were identified at 20 days,60 days,15 months and 3 years old,respectively,with a total of 9 common DEGs in the 4 consecutive groups.The GO functional annotation found that,taking 1-day-old group as the control,1191,2578,1117 and 2835 significant items were enriched in 20-day-old,60-day-old,15-month-old and 3-year-old groups,respectively.Among the top 10 significant GO items in different age groups,there were common ones,as well as unique ones in each age group.KEGG enrichment analysis showed that there were 4,1,3 and 4 unique signaling pathways in the top 30 significant pathways at 20 days old,60 days old,15 months old and 3 years old,respectively,including ECM receptor interaction,cytochrome P450 metabolism of exogenous substances,drug metabolism-cytochrome P450 pathways and other pathways related to abomasum development.The qRT-PCR results were basically consistent with sequencing results,indicating that the sequencing results were rel

关 键 词：不同年龄段 牦牛 皱胃 转录组 发育 代谢 

分 类 号：S823.85[农业科学—畜牧学]